Structural variation is a major driver of genetic diversity and an important substrate for species adaptation and selection. Understanding the relationships between structural variants and functional innovations thus represents a major issue to be addressed. In allopolyploid species, which are common in angiosperms and particularly widespread in crops, exchanges between homeologous chromosomes (i.e. between constituent subgenomes), called HEs for homoeologous exchanges, represent a major source of structural variants. However, we still know little about the genome-wide distribution and resulting functional diversity generated by these variants even though they may have played a prominant role in the evolutionary success of allopolyploidy in plants. In the EDIn project, we will develop an integrated set of analyses to advance knowledge on the causes and consequences of HEs, from the mechanisms responsible for their formation to their effects on gene and genome expression, on chromatin dynamics and plant phenotypic variation in oilseed rape, Brassica napus. Based on highly original plant material specifically designed to promote HE, combined with state-of-the-art multi-omics approaches, our project will address fundamental questions in the context of the allotetraploidy of the B. napus crop genome. EDIn is composed of three main workpackages. WP1 aims to profile the products of inter-homoeologue recombination at very high resolution and build a predictive model of their occurrence, which would be useful in breeding for managing introgressions in crop x wild relative hybrids. WP2 aims to evaluate the global consequences of HEs on gene expression at genome-scale but also at population level. In particular, it will make it possible to characterise the impact of HE on gene regulation networks, which would represent the first in-depth analysis for an allopolyploid crop. WP3 aims to establish the causality of specific HEs by developing an original genetic association study, and to characterize their impact on the reorganisation of the genomic and epigenomic landscapes. In a highly original manner, WP3 will study the changes in the epigenome and the reorganisation of chromatin that introgression of alien chromatin originating from a HE can cause. Our results should therefore prove fruitful in developing useful knowledge and operational strategies for the improvement and diversification of allopolyploid crops, in particular for the management of their genetic diversity or associated genetic resources. This research will be conducted by a consortium of renowned scientists who bring highly complementary expertise, know-how and/or facilities, allowing a more complete understanding of the impact of HEs on the functioning of the allopolyploid genome. One original aspects of this consortium is its direct link to higher education, which represents an excellent opportunity to teach students about the socio-economic impact of public research and train future researchers in the field of recombination, genomics, epigenetics, chromatin organisation and dynamics, for plant breeding.

Fungal pathogens represent a recurrent threat to human health and agriculture and possess extreme adaptive abilities. A major environment-friendly strategy to control fungal diseases is genetic control using naturally resistant crop cultivars. Crop resistance mainly relies on recognition of fungal effectors, key elements of pathogenesis having a dual role in fungal-plant interactions, both targeting plant components and being targeted by resistance (R) proteins and then termed avirulence (AVR) proteins. Breeding cultivars carrying major R genes against pathogens is a common and powerful tool to control diseases. However, the massive deployment of a single source of resistance in the fields exerts a strong selection pressure against avirulent pathogens and the resistance source can be rapidly overcome. There is then an urgent need to improve R gene management to increase their efficiency and durability. The fungus Leptosphaeria maculans causes stem canker of oilseed rape (Brassica napus). The main strategy to control L. maculans is genetic control. However, sources of specific resistance are rare in oilseed rape and studies aim either at identifying new resistance sources to diversify available resources or to optimize the sustainability of available resistances by alternating and/or pyramiding resistances. Partner 1 and 2 of the project have recently determined the 3D structure of four L. maculans AVR effectors (called AvrLm). Surprisingly, three of them are part of a structural family including 13 effectors from L. maculans but also proteins from other plant pathogenic fungi. Our data raise crucial questions, whose clarification could improve resistance gene management: (i) Do secreted effectors, despite their lack of sequence similarity, belong to a limited set of structurally conserved protein families? (ii) Are members of a same effector family targeting the same or similar plant proteins and cellular processes? (iii) Could members of a same effector family be recognized by the same R proteins? The STARlep project aims at exploring structural and functional diversity among L. maculans avirulence proteins to propose knowledge-driven plant resistance management. It is organized in four work-packages: structural characterisation of AvrLm effectors and classification into structural families by looking for structural analogues among L. maculans effectors (WP1), in-depth analysis of the interactions between AVR proteins and their cognate R proteins (WP2), determination of the plant proteins and cellular processes targeted by the AvrLm effector families, and physical understanding of effector-target interactions (WP3), identification of resistances recognizing effectors with contrasted structural patterns and functional mechanisms (WP4). The originality and strength of the STARlep project lie in its interdisciplinarity, involving three teams with internationally acknowledged expertise in the complementary fields of fungal genomics / fungal effector biology (Partner 1) and structural biology (Partners 2 and 3) and a private company developing screening of Brassica material to identify new resistance sources (Partner 4). The STARlep project will generate knowledge on structurally conserved families of effectors, and interaction with cognate R genes and plant targets. STARlep has the potential to impulse the development of resistant crops and of novel strategies to control fungal diseases. A major aim of STARlep is to identify new resistance sources allowing recognition of new effector structural families. The knowledge acquired on structural families of AvrLm effectors will also help us to propose strategies aiming at alternating or pyramiding resistance genes recognizing different classes of effectors, with different types of protein structures. Finally, we will also be able to identify plant targets altered by effectors that could be new targets to control plant diseases.